Probing the role of “power strokes” in a molecular motor with nonequilibrium simulations

An ongoing challenge in chemistry is designing catalysis-driven motors: out-of-equilibrium molecular systems harvesting energy from chemical fuels to bias Brownian motion and exhibit directionality. Alongside their technological potential, artificial molecular motors probe the working principles of their biological counterparts, whose understanding is challenging due to the difficulty of studying their operation in-vivo. However, attempts to design synthetic molecular motors have been led by chemical intuition and chance, with little opportunity to reliably judge their effectiveness or performance until they have been realized experimentally. Moreover, there is a debate in the theoretical literature about whether the origin of directionality in such systems is due to a power-stroke mechanism or an information ratchet mechanism. Here, we introduce a coarse-grained classical approach to explicitly simulate the nonequilibrium dynamics of a catenane-based molecular motor under chemical fueling. We show that simulations reproduce the experimentally probed behavior and can be used as a computational playground to investigate and anticipate the motor’s behavior under design modifications. In particular, our approach confirms that the information ratchet mechanism best describes the system but also shows that introducing powers strokes in the design affects directionality in nontrivial ways, which usual analyses based on chemical reaction networks do not predict.